Monokuma tailors each of his punishments to fit the victim in ways beyond the immediately obvious. For instance, while the connection between the first murderer and their method of punishment is blatant, spending Free Time with Kuwata reveals another layer: Leon frequently skipped practice, feeling he didn't have to go because of his natural talent. Monokuma literally drags him into the batting cage and forces him to stay there until he's finished.
The same goes for the second execution. Mondo is basically a person built on weakness and lies, that is the entire point of his character arc. He was looked down upon for being in his brother's shadow, he lied about his mistake getting his big brother killed, and he couldn't overcome his weakness and finally snapped when Chihiro could. So what does Monokuma do? His punishment, forcing Mondo to ride a motorcycle at speeds that turn him into paste, basically strips Mondo of any presence he has, even his corpse, which Monokuma eats. Even in death Mondo's presence is ineffectual and eventually erased from existence.
Additionally, Mondo can't even kill people from a position of strength. He didn't kill his big brother directly; his big brother died saving his life from a truck he was about to crash into. And he didn't even kill Chihiro on purpose; he lost control of his emotions and doesn't even remember bringing the dumbbell down on Chihiro's head. And, he couldn't even frame another culprit, Genocider Syo, by himself. The main reason chapter 2's trial was so hard was because Byakuya Togami interfered with the crime scene for his own reasons that had nothing to do with Mondo. Finally, he's not even the final Machine Gun Talk Battle in Chapter 2's trial; Kiyotaka Ishimaru has to jump to his defense and fight you in his place. Mondo's influence on the world might as well be pancake butter, even as a murderer!!!
A slightly more meta example: the second execution is based on the tale of "The Story of Little Black Sambo" which, incidentally, is very popular and well-known in Japan. A tale, mind you, about how the humility of the boy prevails over the strength of the tigers.
Similiarly, Chapter 3's execution makes more sense in light of the murderer's character: Celes presents a romanticized front, and wished to go out in a blaze of darkly dramatic glory, an image she tried to mantain at the very end. Monokuma deliberately plays on this, making her believe she's going to die in a suitably gothic fashion — before pulling a bait and switch at the last moment.
There's another possible brilliance if one also reads the manga. Monokuma going for bait-and-switch at Celes was supposed to pull on the despair of Taeko by nailing the fact that she's such a plain person who's hiding behind the romanticized lie of 'Celestia Ludenberg' that her death would be something that's more befitting of a plain person: truck crash.
Chapter 5's execution or at least the "Bad Ending" version of it is called "Detention." As in, a punishment you give to a bad student. And what is the nature of the execution? Being crushed to death by a huge block. What else does a student fear, besides being put in detention by her teacher? Being grounded by her parents! Monobear sadistically made a child's fears of being "grounded" real, by crushing Kirigiri into the ground!
There's also the fact that Kirigiri was late to the trial, so she gets sloooooooooowly carried off to the giant piston. Her secondary "crime" fits the "Detention" name as well.
It goes beyond that. Kirigiri went through the game with a calm and collected presence no matter what happened. Always looking ahead without fear or hesitation. So what does Monobear do? Puts her on a slowly moving conveyor belt facing away from a very loud, constantly moving crusher. Notice how at first she seems to be her usual unshaking self, until you keep hearing the crusher, and seeing the screen vibrate with each crush, as it gets closer and closer but she can't turn around to see it. Watch how her expression changes from stoic, to worried, to terrified and finally to quiet acceptance. The entire thing was meant to finally break Kirigiri's composure.
He also literally crushed Naegi and co.'s chances of solving the mystery and escaping Hope's Peak, via taking away the assistant that helped Naegi to solve the cases when he was stuck.
And even more so: Who created Hope's Peak, gathered the kids first, and then disappeared? Jin Kirigiri aka the Headmaster. And now his daughter and Naegi's closest ally, Kyouko, is the one being executed. That is Monobear's ultimate "fuck you" to both Kirigiris: the one killing the daughter via using a punishment that's very similar to a child's fear of being grounded... is the father's murderer!
When Naegi's strapped into it, the whole thing doesn't fit him nearly as well...which is probably why it doesn't actually kill him at all.
Even the fact that Naegi doesn't have a special Execution is quite suitable when remembers that Naegi had a complex over not being as special as the others
There's more to it! If you look at the board on which the execution name is written, it clearly states that the date of Detention is April 1st - that is, April Fool's day, a day on which people pull tricks on each other. This would point towards the fact that this execution was just devised to fool students into thinking that Naegi was guilty through this trick, when the guilty part is actually Enoshima.
The meaning behind Space Journey execution with the one being executed being the former headmaster and Kirigiri's father can be found in one of the Monokuma Theatres, far sooner than one would be able to decode it. Specifically, Act IV, long before we discover who the victim was. Remember, the headmaster was the one who came up with the idea of sealing everyone inside the school to begin with. Monokuma uses a spaceship as a metaphor for the school in Act IV, saying everyone is on a trip in space and is far away from the earth. What is the headmaster sealed inside? A spaceship.
To add to that, its stated in later material that Jin Kirigiri was inadvertently responsible for letting Enoshima get away with everything due to his love for talent. His death literally has him being shot into the stars and then forcibly pulled back to earth.
Even Mukuro's execution is ironic. She was the Super High-School Level soldier, who had never received a single wound on the battle field. Her Execution involves being wounded so many times she dies. Also, she was a soldier betrayed by her comrade.
Doubly so when you consider that it's not uncommon for solders to refer to themselves as brothers-in-arms. Who betrayed Mukuro? Her own sister!
In Case 3, Celes is very obvious about being the murderer. It seems odd when she is supposed to be a good liar and have overall decent luck, what with her being a "Super High-School Level Gambler". However, this makes much more sense when you realize she's up against Naegi, who is specifically stated to have "Super High-School Level Good Luck". To put it in poker terms, she just got dealt only a pair of twos while Naegi has a royal flush — you can only bluff so far with that. In one of Celes's Free Time conversations, she discloses to Naegi that the most important thing behind being a Super High-School Level Gambler is luck. So, when she came against someone said to have luck as his one and only talent, she lost.
All the way back in Chapter 1, Junko broke a rule, and Monobear killed her by summoning spears of Gungnir. This notably happens before the first execution, where we find out that Monobear tailors the executions to the culprit. Given that Junko didn't murder anyone and got killed in such an unfitting way can be chalked up to that it's not a trial, and any other inconsistencies (such as her choice of words) can be explained away. However, if "Junko" was a soldier who took part in a mercenary group called Fenrir, and conspired with the mastermind as a fellow SHSL despair, then this is put into a whole new light! Leon wasn't the first execution: Mukuro Ikusaba is! And given her choice of words, it's likely that she was betrayed by the mastermind.
Especially fitting is the name of the weapon. Gungnir. The spear of Odin, which he is fated to use in the battle of Ragnarok to stab Fenrir.
Then, to delve further into Norse Mythology, Fenrir's sibling Hel is half-living and half-dead... or, in some versions, half black and half white.
FridgeNightmare Retardant? In Chapter 6 we find the cold storage where all the mutilated corpses of the victims are stored.. which must include that tub of Mondo butter.
The final execution pauses at the very last second before killing its victim. Why? [SPOILERS AHEAD] Junko has a fetish for despair. She was smiling throughout all the executions, but she has a puzzled expression when the crusher doesn't fall on her. The pause was for getting rid of all the accumulated despair before going for the kill.
Adding to this, the pause is very short, only long enough for Junko to get that puzzled expression. If it had waited any longer, she likely would have begun to feel despair over not being killed. Similarly, it mirrors the way Mukuro Ikusaba was killed, as both of them felt confusion before they died; Mukuro because she didn't think she would be killed, and Junko because she thought she would.
In Chapter 3, Ishimaru goes through a massiveHeroic BSOD after it was revealed in the previous chapter that Mondo was the murderer, and was executed as a result. In a Free Time segment, Ishimaru reveals to Naegi that he's never managed to make a single friend or even carry a regular conversation with anyone before. When you take that into account, it's no wonder that Ishimaru was so affected by Mondo's death; Mondo was the first real friend Ishimaru had ever made, he turned out to be a murderer, and was subjected to a Cruel and Unusual Death immediately afterwards.
During trial 5, you have a chance to throw Kirigiri under the bus or bluff for her. Should you point out her contradiction, you get the bad ending. If you bluff, Naegi is nearly executed but you get the good ending. It might seem like unfortunate implications at first but if you think about it, what is Naegi's SHSL title?
On the bad ending; Naegi, Togami, Hagakure and Asahina are all shown being alive and with children, with Fukawa being the only one who is shown as passed away. On an initial playthrough, this may just seem like an arbitrary choice... until you get to chapter 6, where it's revealed that Genocider Syo actually remembers the circumstances of The World's Most Despair-inducing Incident in the History of Mankind. So what would the best way to keep that secret from being revealed to the surviving students? Murdering Fukawa, and thereby killing Syo at the same time, thus preserving the secret!
Despite being a serial murderer, Genocider Syo never murders anyone, despite the others' fear of her - because she knew about the current state of the world and didn't actually want to leave the school.
Plus, she herself says that the point of murdering inside the school is to NOT GET CAUGHT. Killing the way she always does would mean they will surely know it's her real quickly, and she doesn't want to kill any other way.
A related bit of fridge horror is addressed in Genocider Syo's free time events - why Genocider Syo didn't kill Togami (or anyone else, for that matter) during the two-year time gap. She mentions that Togami is the first person she's fallen for who she hasn't had an urge to kill, and that she'd give up killing if she could be with him.
Also, after the cast discovers Fujisaki was a boy, Syo exclaims that she "should have killed him first." This comes after arguing that she wouldn't have killed anyone while trapped in the Closed Circle of the school. It seems with the reveal that she was actually wishing she'd killed Fujisaki during the "normal" time at Hope's Peak.
A couple involve the trial decor:
Ch. 3's courtroom is decorated with with blue wallpaper and moons. Of course there would be a celestial theme to the trial where Celestia is the culprit.
Ch. 5's courtroom is eye-searing, being colored with a clashing checkerboard of hot pink and puke green. Considering that the Ch. 5 murder was staged, it only makes sense that there'd be something "off" about its corresponding courtroom.
The manga did a lot of Alternate Character Interpretation that does good to sympathize both Kuwata and Celes, and they're making a lot of sense that there was no way for Naegi to know how Kuwata was getting the screwdrivers not to hunt and kill Maizono, but to calm her down (in vain), and compounding that, Kuwata has troubles in spitting out that fact it's the reason why he did that due to panic, or the fact that regardless of what he tells, he's screwed either way. Likewise, Celes only keeps things for herself, tell mostly lies or plagiarized stories to others, and there was no way Naegi could realize what she was like when she was Taeko and how she was suffering due to her unremarkableness and must keep the charade of Celestia Ludenberg at all cost, leading to become really greedy and commit the double-murder. While that wouldn't absolve them from murder, all of it could still be happening in canon, and the canon series being in Naegi's POV prevents us to realize them right off bat.
In the final Class Trial it seems that Junko is copying some of the surviving students' personalities. When she is in her "princess" personality, with a Cool Crown to boot, it's similar to Togami's (SHSL Heir) arrogant personality, her punk persona is similar to Genocider's loud and aggressive personality (don't forget the tongue), when she puts on glasses and becomes Ms. Exposition, her tone and how she says it is similar to Kirigiri's analytic personality, then followed by Asahina's cutsy personality (when she talks about donuts and proteins), and afterward has Fukawa's depressing personality.
The ones that doesn't fit are her "Dio Brando" personality, her Monokuma personality, and her final one, a blank, emotionless one; plus her Villainous Breakdown expressions. Now, the first two are respectively something that could scare Hagakure, and (obviously) Monokuma; but the third one is used in response to Naegi declaring that nobody will fall into Despair. This is when Enoshima ''stops'' playing charade and assumes a truly "Despair" persona: it's Hope vs. Despair, and she's going against the Super High-School Level Hope. The blank Ultimate Despair persona may very well be the true self. It's the equivalent of The Joker dropping all humor and theatricality in his behavior and showing the emptiness and raw, hateful malevolence that's always been at the core of this sick, sick person.
At first, Junko Enoshima's death seems weird, and not just because she's the only student who is neither murdered by another student or executed. Of course, this strange death foreshadows who the mastermind is, but there's something else. Monobear is the one who charged at Junko and she just held him down with her foot. It really doesn't seem like an act of violence against the headmaster. Then, at the end of the game, we learn that the "Junko" back then was really Mukuro Ikusaba, Junko's twin sister. When asked by the others why she killed her own sister, Junko flippantly remarks that it was because she was a bad actress. Junko murdered her sister on a whim, in order to prove a point to the others. No wonder Monobear instigated the whole thing! Also, according to IF, Junko would've had the trial rules explained on that day even if nobody had been murdered yet (though one would think that the murders she wanted would be more likely before anyone knew that graduating would cost everyone else's lives) and gave Mukuro a script to follow that involved stomping on Monobear and didn't end in impalement. There was quite a bit of premeditation involved.
The end-of-day Theater where Monobear rambles on about how things like war and pollution immediately sound better when you tack a -chan on the end. Once revealed, Junko occasionally refers to her dead sister as "Mukuro-chan." What does that come out to, given her Meaningful Name? "Corpse-chan."
In chapter 6, when photographs are given out containing all students but the ones that they were given too the reason that they aren't in them is that they were the ones taking the photos.
The reason that Junko's surname is different from her sister, may be that it is a stage name. Enoshima is also the name of a 'Picturesque island' near Tokyo. It's also quite possible that Mukuro Ikusaba is another codename. "Mukuro Ikusaba" can translate to "Corpse Warblade;" Mukuro was a highly skilled soldier who worked for the mercenary group Fenrir. The fearsome and cool-sounding "Mukuro Ikusaba" could be an alias or a nickname she went by during her days with Fenrir.
Celes said that if she's reincarnated she'd be Marie Antoinette... and it actually held more than 'ending up getting executed again'. Celes have been trying to invoke the image of Marie Antoinette even throughout her life, starting from her extravagant life and dream, as well as doing horrible things that would cause her to be hated and villified by those around her (as seen by Asahina in the game), and decided to Face Death with Dignity. And it even goes meta: when Celes' reasoning was first revealed, a lot of fans would accuse her as a shallow murdering bitch like how Antoinette got all those... degrading insults. However, as time passed, with Monokuma doing a lot more despicable things and other interpretations of Celes (the manga, especially) were revealed, opinions on Celes has softened up, kind of like how the more recent discoveries that Antoinette wasn't as much as a bitch she was accused of, and how her executors also doing worse things than what they accused her for... helped fixing her reputation.
The barred windows and vault to the main entrance. Yes, if the students woke up with no memory and told they were trapped in there for demented purposes, they would believe them. However, upon further inspection, the screws and nuts are on the inside. Since they locked themselves in the school to survive the Despair, that'd make sense.
There are actually two hints very early on that Mukuro is posing as Junko Enoshima and assisting her. When the students all first assemble in the gym, Mukuro is the one to point out that the students cellphones are missing. The second hint comes when Sakura tells Mukuro that she doesn't look the same as Junko Enoshima does in the magazines. Mukuro laughs this off and states that the pictures in the magazines are photo shopped, and the issues isn't pressed any further. In retrospect, maybe Junko made the right decision in killing Mukuro because she wasn't a good enough fake.
In IF, the mastermind briefly pretends to be a Hope's Peak upperclassman named "Besshiki Madarai." In Dangan Ronpa Zero, there's a Hope's Peak student that is an upperclassman named Isshiki Madarai who is part of a set of octuplets with 1-8 based Numerical Theme Naming (Isshiki, Nishiki, Mishiki, Yoshiki, Goshiki, Rokushiki, Shichishiki, and Yasshiki).
According to one of the sidestories, Naegi wasn't actually the initial winner of the lottery, that being a girl who's pass into the Academy was inadvertently destroyed by Naegi's actions, forcing them to redo the lottery. Seems irrelevant until one realises that this creates a dark Call Forward to the Chapter 5 Trial, where something very simular happens between Kirigiri and Naegi. And, like before, the trial has to be redone, this time with Naegi winning.
At first, Fukawa's sudden infatuation towards Togami comes out of nowhere, especially since there had been no hints towards it bar them standing next to each other in crowd scenes. Then I read Dangan Ronpa Zero and it hit me when, at the end [SPOILERS FOR DANGAN RONPA ZERO] Enoshima states her love for Matsuda was so strong that it survived even her losing her memories. Who's to say the same thing isn't true for Fukawa? Better when you realise that its indicated she was in love with him during the students normal time at Hopes Peak.
Hagakure's Tohoku Regional Accent is largely associated with country bumpkins. In one free time event, though Celes maintains her parents were European, she admits she was raised in Tochigi, another comparatively rural part of Japan. Then her chapters in the manga show her desperation to escape the "mediocrity" of her life as Taeko Yasuhiro by reinventing herself as a glamorous sophisticate. No wonder she dislikes Hagakure so much—even his first name's a reminder of what she's trying to leave behind.
During the talk between Monokuma and Sakura Oogami about the 16th student. Monokuma joke about not giving his three sizes. At first, it seems like another stupid joke of his. But then, Fridge Brilliance kick in during Case 6, it was Junko Enoshima's and Mukuro Ikusaba's three sizes that put a connection between those two and helped Naegi realize Mukuro is the one who died instead of Junko during her supposedly death.
The cafeteria is always locked at night. Probably because it's when Enoshima is getting her meals. This also explains why Monokuma is almost never seen at night.
Monokuma mocks Naegi for getting the room with the bathroom door with the unaligned doorknob, calling it ironic that the so call "Super High-School Level Good Luck" student would have that kind of room. Later, this bit of "bad luck" is what not only proves his innocence in the first trial, it helps reveal the real culprit. This entertains the idea that Naegi's "bad luck" may really be "good luck" in disguise.
When you stop and think about the remaining students, they all have one major thing in common. They were all accused of murder at least once. Naegi was accused in the first trial, Genocider Syo and Togami in the second, Hagakure in the third, Asahina in the fourth (including Hagakure and Touko), and Kirigiri in the fifth. An interesting deduction to make that you probably wouldn't catch your first time around.
In Case 1, before the murder actually happens, everyone makes a big deal about what bullshit Monobear is spouting if he actually thinks the students would ever resort to murder. Besides, Naegi thinks, they all seem like such nice people, don't they? (Oowada's bad temper, Fukuwa's paranoia, and Togami's jerkass tendencies aside.) Well obviously, a murder does happen, but that's obvious when it comes to this game. The Fridge Horror kicks in when Monobear executes Leon Kuwata, the first murderer: everyone crowds around to watch the execution up close! Everyone! Nobody tries to stop the baseball machine from beating Leon to death, nobody throws up, nobody even averts their eyes. They just...stand there, like members of a lynch mob who aren't actually participating in the lynching. Certainly they all call Monobear a monster, say this is too cruel, etc., but that's after the execution is over. While it's happening, they all crowd around outside the batting cage like solemn judges. This is the player's first clue that all the students are capable of murder, and thus everyone is a suspect in every case.
Or, more likely, they were too horrified to act. There is such a thing as being shell-shocked, and it was a particularly heinous death.
What would happen to Maizono if she suceeds in framing Naegi? She will learn how her friends in the idol group died and nothing more. Because Monobear gave a Literal Genie question in the video. If she is released into the outside world, she might have to find out about their death by herself.
In Case 4, Alter Ego's execution inolves it getting compacted into a metal ball by getting smashed by an excavator's claw., which is bad enough on its own. But Monobear made it worse by making an offhand comment about not wanting it to go to waste, implying it was originally meant for someone else. Considering the events just prior to the murder, that was supposed to be Sakura's execution.
Oh, ho, it's even worse than you let on. You notice how Alter Ego was destroyed with demolition equipment? It's very likely that Monobear was going to wring the maximum amount of despair out of Sakura by destroying her along with her most cherished family heirloom: the 300-year old dojo, the very same one she tried to protect by assisting Monobear.
Speaking of which, with the revelation of the mayhem in the outside world, what are the chances that the dojo has already been destroyed?.
Chapter 5's bad ending. It's actually set up like a happy ending at first: after Kirigiri is executed, the murders stop for good. So everyone lives life in bliss inside the school, as depicted in a photograph you see while Naegi is narrating. What makes it both "fridge" and "horror" creeps in through three ways: first, Naegi, Togami, Asahina, and Hagakure are alive in the photograph, but Fukuwa is not, she's just a photograph like all the previously killed students. It's never explained whether Fukuwa was killed, committed suicide, or was executed. Second, the murders may have stopped and life in the school may be happy, but these students were all Super High-School Level talented when they arrived, which means they're trapped in a gilded cage where the world can never appreciate their potential. Third, there are three children in the photograph. A boy by Togami, a toddler by Naegi, and an infant by Hagakure. The thing is, Fukuwa is dead...which means Asahina is the only one who could've given birth to the children...which means Asahina is continuing the students' family trees inside the school by herself! Although that last one might be less Fridge Horror if you interpret the situation as Asahina making the best out of the situation as it's possible, and thus having three men to herself in a sort-of harem.
Also, Aoi so far has only given birth to boys. (Unless Fukawa was the Missing Mom of one of them). Which means potentially they're gonna have to keep trying to get a girl, if they want to continue their bloodlines. Incest ahoy.
You're also forgetting that the air purifying machine will stop working when Junko dies. Though she might live longer than the remaining students, she won't live forever. And then those kids that only knew life inside the school would have to leave or suffocate inside.
You saw the Fridge Brilliance entry about the last execution? If no-one deliberately tampered with the crusher, then Junko (or rather her Monobear personality) deliberately designed that Hope Spot to deny herself despair. She's that fucked up.
Actually, someone may have. Alter Ego has already shown that he/she/it can tamper with executions when he/she/it stopped the crusher during the Chapter 5 punishment. Who's to say Alter Ego didn't want to give Junko her the last bit of despair before her demise?
Everyone is wearing clothes that are either casual or the uniform of a different school, despite having all been shown in the past as wearing the Hope's Peak uniform. There's no real reason for all of them to have changed into their old clothes, so Junko must have stripped and redressed them to keep up the illusion that they had not yet been to the school.
Mercifully not the case. The headmaster's videos show that they redressed themselves into their game outfits of their own will after the WMDIEitHoM hit.
This point also leads to some Fridge Logic: How did nobody notice that they aged two years? Considering almost all of them are teenagers, they should have grown a lot in that time.
It's actually hinted that some of them did notice. Though it's never explicitly spelled out, it's likely that this is what Kirigiri was talking about when she asked Monokuma what he did to her body at the end of Chapter 3. Sakura also mentions that something has happened to the students' bodies in her final note, which causes Monokuma to stop reading it immediately.
But taking this further, why did Ikusaba Mukuro's measurements match the ones in her student profile? The school shut down a year before the game, so she should have grown from that time, right? Yet Kirigiri says that they were an exact match. It would be acceptable if her height had finished growing by that age, but not her other measurements.
At the end of the game, the chickens in the fifth floor greenhouse most likely suffocated and died when the surviving students left - unless they remembered them and went back to get them, which is unlikely.
One bit of fridge horror sets in once you learn about the two years of missing memories the students had. Some of the photographs found during Chapter 6 suggest that Genocider Syo was both active and infatuated with Togami even back then. Given what Syo usually does to guys she likes, how did Togami manage to survive long enough to get locked in the school in the first place?
This question does get answered during Genocider Syo's free time events, as seen in the Fridge Brilliance entry above.
Maizono's first case of "good intuitions" is telling Naegi that she's not a doll—"I'm very much alive!" Apparently she's that used to people thinking of her as a pretty face, not a person.
Seeing all of both "regular" Fukawa and Genocider Syo's free time events reveals that Syo eventually traveled all the way to Shikoku to kill the boy who publicly humiliated Fukawa in elementary school.
The good ending of the Lighter and Softer School Mode/Dangan Academy is rife with this. Usami causes a time paradox to beat the stuffing out of Monokuma, and everyone lives and promises to stay friends after they leave the school. But they still don't know who was behind Monokuma, they have no idea about their missing memories, Kirigiri's father is probably still bones in a box, and they're likely to get an exceedingly unpleasant surprise once they see what's happened to the outside world.
When Genocider Syo is introduced, she calls herself the SHSL Serial Killer, which implies that the staff at Hope's Peak knew about Fukawa's split personality and gave her the title. In addition, this implies that the staff covered up the fact that there is a serial killer among the student body and were possibly studying her regardless of the lives she's endangering and/or took. This is worse when you read Dangan Ronpa Zero and realise this is exactly the sort of things the staff would do.
Speaking of the school staff, it's implied in (at least the translation of) School Mode that Ishimaru's grandfather was a Hope's Peak alumnus, as he's described as "the official Ultimate Manager." In that case, while he fulfilled the school's reputation for guaranteed success by becoming prime minister, he crashed and burned soon afterward. Maybe they just couldn't save him from himself or whatnot, but given all the other questionable things the academy's canonically been up to, you've got to wonder how long they've been turning out screwed-up prodigies.
During the last class trial, the students determine that the Puppetmaster must be inside the school because Monokuma's Control Room is inside Kibougamine Academy. Since that was the case, why did the students need to determine Ikusaba Mukuro's killer before discovering who was the Puppetmaster or why did they begin to blame Naegi? Through logical deduction, the Puppetmaster was controlling Monokuma during the first trial, which means that only Sayaka Maizono or Junko Enoshima could be the Puppetmaster.
Before they realized Ikusaba Mukuru was disguised and died as Junko Enoshima, it was possible she was controlling Monokuma at the time, since she was also a Super High School Level Despair.
Monokuma is forcing them to do it in that order. At the one point where they do try and skip ahead and discuss who the mastermind is Monokuma interjects and tells them they need to solve Mukuro's murder first. It sort of helps that they have already figured out the Puppetmaster is the last killer.
Even given that gender roles are more strictly enforced in Japan than in the West, how the heck did presenting as female allow Chihiro to (implicitly) escape all gender-based bullying from the time he started to when he entered Hope's Peak? Wouldn't some female bullies have gone after him for some non-reason? And depending on when Chihiro began presenting as female, why did none of his tormentors recognize him?
For the recognition, it's completely possible that Chihiro is that good of a crossdresser. Either that, or perhaps Chihiro stopped presenting himself as a girl during his time attending Hope's Peak. As for the gender roles being strictly enforced, it's basically been heavily implied, if not outright stated, that Hope's Peak doesn't care who its students are or not. As long as they meet the age requirements and have proper talent, they're allowed into the Main Course. While this may not have avoided as Chihiro's Electro ID (if they even had that back then) from classifying him as male, it may have allowed him to avoid the staff there from questioning the situation of his crossdressing.
On the fifth floor, there's a classroom that looks like the site of a massacre, something that the students deduce, with Monokuma stating that he did not alter the room. Only problem, Dangan Ronpa Zero infers that the event being referred to happened in the old school building, which the game very clearly does not take place in. Furthermore, with the revelation that the students locked themselves in, how is a bloody classroom even there? The Steering Committee was willing to commit brainwashing and outright murder to keep the incident under wraps. Given how the students spent a whole year in the school, why wasn't the room cleaned and why would what was supposed to be a shelter have the site of a massacre there?
Celestia has an in-story fridge logic moment in School Mode when she wonders aloud who exactly has been preparing the meals for the 15 students (the assumption in the main story being that the students are given the ingredients and make everything themselves). She brings up the possibility of Monokuma doing it, when in the main story we find out that the machine is just an extension of Junko (while this version of reality starts up mainly because there's only one Monokuma around, and he needs the students to build back-ups for him). If it really is Junko doing it while the cafeteria is locked up, one wonders when she sleeps.